[gmx-users] PBC problem in bilayer system

[shahab shariati]

Dear Justin


I did following:


trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9

Based on your reply*, *I translated all system along the z.

I used x and y according to box dimension.

I used 9, instead of z dimension (8.30034), for z.

When I see **.xtc using vmd, problem was not solved.

Should I increase or decrease z value for -trans option?

Please see the following link:

https://www.dropbox.com/s/ocahn2yzudwcj3z/figure%203.TIF?dl=0